Importance of hydrogen bonding and aromaticity indices in QSAR modeling of the antioxidative capacity of selected (poly)phenolic antioxidants

QSPR Modeling and Experimental Determination of the Antioxidant Activity of Some Polycyclic Compounds in the Radical-Chain Oxidation Reaction of Organic Substrates

The present work addresses the quantitative structure−antioxidant activity relationship in a series of 148 sulfur-containing alkylphenols, natural phenols, chromane, betulonic and betulinic acids, and 20-hydroxyecdysone using GUSAR2019 software. Statistically significant valid models were constructed to predict the parameter logk7, where k7 is the rate constant for the oxidation chain termination by the antioxidant molecule. These results can be used to search for new potentially effective antioxidants in virtual libraries and databases and adequately predict logk7 for test samples. A combination of MNA- and QNA-descriptors with three whole molecule descriptors (topological length, topological volume, and lipophilicity) was used to develop six statistically significant valid consensus QSPR models, which have a satisfactory accuracy in predicting logk7 for training and test set structures: R2TR > 0.6; Q2TR > 0.5; R2TS > 0.5. Our theoretical prediction of logk7 for antioxidants AO1 and AO2, based on consensus models agrees well with the experimental value of the measure in this paper. Thus, the descriptor calculation algorithms implemented in the GUSAR2019 software allowed us to model the kinetic parameters of the reactions underlying the liquid-phase oxidation of organic hydrocarbons.

Hybrid Classification/Regression Approach to QSAR Modeling of Stoichiometric Antiradical Capacity Assays' Endpoints

Quantitative structure-activity relationships (QSAR) are a widely used methodology allowing not only a better understanding of the mechanisms of chemical reactions, including radical scavenging, but also to predict the relevant properties of chemical compounds without their synthesis, isolation and experimental testing. Unlike the QSAR modeling of the kinetic antioxidant assays, modeling of the assays with stoichiometric endpoints depends strongly on the number of hydroxyl groups in the antioxidant molecule, as well as on some integral molecular descriptors characterizing the proportion of OH-groups able to enter and complete the radical scavenging reaction. In this work, we tested the feasibility of a "hybrid" classification/regression approach, consisting of explicit classification of individual OH-groups as involved in radical scavenging reactions, and using further the number of these OH-groups as a descriptor in simple-regression QSAR models of antiradical capacity assays with stoichiometric endpoints. A simple threshold classification based on the sum of trolox-equivalent antiradical capacity values was used, selecting OH-groups with specific radical stability- and reactivity-related electronic parameters or their combination as "active" or "inactive". We showed that this classification/regression modeling approach provides a substantial improvement of the simple-regression QSAR models over those built on the number of total phenolic OH-groups only, and yields a statistical performance similar to that of the best reported multiple-regression QSARs for antiradical capacity assays with stoichiometric endpoints.

Computational Investigation of the Antioxidant Activity of Dihydroxybenzoic Acids in Aqueous and Lipid Media

Reactive free radicals have both beneficial and destructive effects. Indeed, at physiological levels, free radicals help to preserve homeostasis by acting as signal transducers. However, excessive generation of free radicals can harm and damage membranes, proteins, and DNA, among other cell structures. Dihydroxybenzoic acids (DHBAs) have proven their antioxidant capacity against a large variety of free radicals, as well as their ability to inhibit or restrict reactive species overproduction. In this paper, a computational analysis of the antioxidant activity of a series of DHBAs in polar and nonpolar media was carried out at the DFT/M06-2X/6-[Formula: see text] level of theory. The implicit SMD solvation model was used in order to rationalize the experimental findings and to investigate the solvent effect on the mechanism and the radical scavenging ability. The obtained results put in evidence that HAT is the predominant mechanism in nonpolar media, whereas SPLET is more favored in polar environment. The BDE[Formula: see text], [Formula: see text], and [Formula: see text] descriptors are used to predict the most reactive hydroxyl groups and the antioxidant activity order of the studied DHBAs. Our results are in total agreement with experimental findings (inhibition of lipid peroxidation and scavenging of hydrogen peroxide). Moreover, this study shows that the substitution of the hydrogen atom by strong electron-donating groups, namely NMe2, in the ortho positions of the best experimental DHBAs leads to a significant enhancement of their antioxidant activity.

Density functional theory studies of the antioxidants-a review

The following review article attempts to compare the antioxidant activity of the compounds. For this purpose, density functional theory/Becke three-parameter Lee-Yang-Parr (DFT/B3LYP) methodology was carried out instead of using pharmacological methodologies because of economic benefits and high accuracy. This methodology filtrates the compounds with the lowest antioxidant activity. At first, the Koopmans' theorem was carried out to calculate some descriptors to compare antioxidants. The energy of the highest occupied molecular orbitals (HOMO) was accepted as the best indicator, and then some studies confirmed that the highest occupied molecular orbital/lowest unoccupied molecular orbital (HOMO-LUMO) energy gap is the more precise descriptor. Although it would be better to compare spin density distribution (SDD) on the oxygen of the corresponding radical in the polarizable continuum model (PCM) to evaluate their capability to chain reaction inhibition. Next, it was mentioned that in the multi-target directed ligands (MTDLs), the antioxidant is connected to other moieties in para positions to create better antioxidants or novel hybrid compounds. Indeed, SDD was introduced as a descriptor for MTDL antioxidant effectiveness. Then, the relation between antioxidants and aromaticity was investigated. The more the aromaticity of an antioxidant, the more stable the corresponding radical is. Subsequently, in preferred antioxidant activity, it was defined that the hydrogen atom transfer (HAT) mechanism is more favored in metabolism phase I. It has been seen that the solvent model can change the antioxidant mechanism. Therefore, the solvent model is more important than the chemical structure of antioxidants, and an ideal antioxidant should be evaluated in PCM for pharmacological evaluations.

A Statistically Supported Antioxidant Activity DFT Benchmark-The Effects of Hartree-Fock Exchange and Basis Set Selection on Accuracy and Resources Uptake

Polyphenolic compounds are now widely studied using computational chemistry approaches, the most popular of which is Density Functional Theory. To ease this process, it is critical to identify the optimal level of theory in terms of both accuracy and resource usage—a challenge we tackle in this study. Eleven DFT functionals with varied Hartree–Fock exchange values, both global and range-separated hybrids, were combined with 14 differently augmented basis sets to calculate the reactivity indices of caffeic acid, a phenolic acid representative, and compare them to experimental data or a high-level of theory outcome. Aside from the main course, a validation of the widely used Janak’s theorem in the establishment of vertical ionization potential and vertical electron affinity was evaluated. To investigate what influences the values of the properties under consideration, linear regression models were developed and thoroughly discussed. The results were utilized to compute the scores, which let us determine the best and worst combinations and make broad suggestions on the final option. The study demonstrates that M06–2X/6–311G(d,p) is the best fit for such research, and, curiously, it is not necessarily essential to include a diffuse function to produce satisfactory results.

Polarizability and aromaticity index govern AhR-mediated potencies of PAHs: A QSAR with consideration of freely dissolved concentrations

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous environmental pollutants associated with adverse human effects including cancer, and the aryl hydrocarbon receptor (AhR) is a key ligand-activated transcription factor mediating their toxicity. However, there is presently a lack of data on AhR potencies of PAHs. Simple, transparent, interpretable and predictive quantitative structure-activity relationship (QSAR) models are helpful, especially with the consideration of freely dissolved concentrations linked to bioavailability. Here, QSAR models on AhR-mediated luciferase activity of PAHs were developed with nominal median effect concentrations (EC₅₀, _nom) and freely dissolved concentration (EC_{50, free}) as endpoints, and quantum chemical and Dragon descriptors as predictor variables. Results indicated that only the EC_{50, free} model met the acceptable criteria of QSAR model (determination coefficient (R²) > 0.600, leave-one-out cross validation (Q_LOO²) > 0.500, and external validation coefficient (Q_EXT²) > 0.500), implying that it has good goodness-of-fit, robustness and external predictive power. Molecular polarizability and aromaticity index reflecting the partition behavior and intermolecular interactions can effectively predict AhR-mediated potencies of PAHs. The results highlight the necessity of adoption of the freely dissolved concentration in the QSAR modeling and more in silico models need to be further developed for different animal models (in vivo or in vitro).

Synthetic phenolic antioxidants: Metabolism, hazards and mechanism of action

Synthetic phenolic antioxidants can interact with peroxides produced by food. This paper reviews correlation between BHA, BHT and TBHQ metabolism and harms they cause and provides a theoretical basis for rational use of BHA, BHT and TBHQ in food, and also put some attention on the transformation and metabolic products of PG. We introduce BHA, BHT, TBHQ, PG and their possible metabolic pathways, and discuss possible harms and their specific mechanisms responsible. Excessive addition or incorrect use of synthetic phenolic antioxidants results in carcinogenicity, cytotoxicity, oxidative stress induction and endocrine disrupting effects, which warrant attention. BHA carcinogenicity is related to production of metabolites TBHQ and TQ, and cytotoxic effect of BHA is the main cause of apoptosis induction. BHT carcinogenicity depends on DNA damage degree, and tumour promotion is mainly related to production of quinone methylation metabolites. TBHQ carcinogenicity is related to induction of metabolite TQ and enzyme CYP1A1.

Radical scavenging activity of hydroxycinnamic acids in polar and nonpolar solvents: A computational investigation

The aim of this work is to perform a computational study of the radical scavenging activity of a series of common hydroxycinnamic acids (HCAs) in polar and nonpolar solvents in order to rationalize the experimental order obtained in ethanol and to analyze the solvent effect on mechanism and radical scavenging capacity. The thermodynamics of the main mechanisms, namely, hydrogen atom transfer (HAT), sequential proton loss followed by electron transfer (SPLET), and single electron transfer followed by proton transfer (SET-PT) were investigated at the M05-2X/6-31[Formula: see text]G([Formula: see text]) level of theory using the SMD solvation model. This study shows that the SET-PT mechanism is disfavored in all media, whereas HAT is the most thermodynamically favored mechanism in gas phase and SPLET is the preferred reaction pathway in pentyl ethanoate, ethanol and water. The thermodynamically preferred site of antioxidant action and the radical scavenging order are predicted using the BDE[Formula: see text] and (PA[Formula: see text]ETE)[Formula: see text] descriptors corresponding to the HAT and SPLET mechanisms, respectively. The obtained results point out that the mechanism and the radical scavenging potency are influenced by solvent polarity and our predictions are in agreement with the experimental measurements performed in ethanol giving the following descending order: caffeic [Formula: see text] [Formula: see text] [Formula: see text]-coumaric acid. Our results also show that the ortho substitution of caffeic acid by strong electron donating groups leads to a notable increase of their radical scavenging activity and new potent HCA derivatives are designed.

Flavones' and Flavonols' Antiradical Structure-Activity Relationship-A Quantum Chemical Study

Flavonoids are known for their antiradical capacity, and this ability is strongly structure-dependent. In this research, the activity of flavones and flavonols in a water solvent was studied with the density functional theory methods. These included examination of flavonoids’ molecular and radical structures with natural bonding orbitals analysis, spin density analysis and frontier molecular orbitals theory. Calculations of determinants were performed: specific, for the three possible mechanisms of action—hydrogen atom transfer (HAT), electron transfer–proton transfer (ETPT) and sequential proton loss electron transfer (SPLET); and the unspecific—reorganization enthalpy (RE) and hydrogen abstraction enthalpy (HAE). Intramolecular hydrogen bonding, catechol moiety activity and the probability of electron density swap between rings were all established. Hydrogen bonding seems to be much more important than the conjugation effect, because some structures tends to form more intramolecular hydrogen bonds instead of being completely planar. The very first hydrogen abstraction mechanism in a water solvent is SPLET, and the most privileged abstraction site, indicated by HAE, can be associated with the C3 hydroxyl group of flavonols and C4’ hydroxyl group of flavones. For the catechol moiety, an intramolecular reorganization to an o-benzoquinone-like structure occurs, and the ETPT is favored as the second abstraction mechanism.

Predictive QSAR modeling for the antioxidant activity of natural compounds derivatives based on Monte Carlo method

In this research, QSAR modeling was carried out through SMILES of compounds and on the basis of the Monte Carlo method to predict the antioxidant activity of 79 derivatives of pulvinic acid, 23 of coumarine, as well as nine structurally non-related compounds against three radiation sources of Fenton, gamma, and UV. QSAR model was designed through CORAL software, as well as a newer optimizing method well known as the index of ideality correlation. The full set of antioxidant compounds were randomly distributed into four sets, including training, invisible training, validation, and calibration; this division was repeated three times randomly. The optimal descriptors were picked up from a hybrid model by the combination of the hydrogen-suppressed graph and SMILES descriptors based on the objective function. These models' predictability was assessed on the sets of validation. The results of three randomized sets showed that simple, robust, reliable, and predictive models were achieved for training, invisible training, validation, and calibration sets of all three models. The central decrease/increase descriptors were identified. This simple QSAR can be useful to predict antioxidant activity of numerous antioxidants.

Fragmentation method reveals a wide spectrum of intramolecular hydrogen bond energies in antioxidant natural products

Very strong and weak IHBs in curcumin.

What is responsible for antioxidant properties of polyphenolic compounds from plants?

Due to the negative impact of reactive species (including free radicals) on humans and animals, the investigations to find effective substances (antioxidants), which protect living organisms against their damaging influence are carried out throughout the world. As most widespread synthetic antioxidants are suspected of having a noxious effect on the human body, more and more attention is paid to natural antioxidant compounds found in plants (especially phenolic compounds). The aim of this paper is to present the data about antioxidant activity of polyphenolic compounds with the emphasis on the main factors having influence on their antioxidant activity: chemical structure, ability to form hydrogen bonds, capability of metal ions chelation and reduction, adduct formation, kinetic solvents effect, mechanism of antioxidant reaction, capability of antioxidant enzyme activation and reduction potential.

Biological Potential of Novel Methoxy and Hydroxy Substituted Heteroaromatic Amides Designed as Promising Antioxidative Agents: Synthesis, 3D-QSAR Analysis, and Biological Activity

This paper discusses antioxidative and biological activities of 25 novel amidino substituted benzamides with a variety of heteroaromatic nuclei attached to the benzamide moiety and with a variable number of methoxy or hydroxy substituents. Targeted compounds, bearing either amidino or 2-imidazolinyl substituent, were obtained in the Pinner reaction from cyano precursors. 3D-QSAR models were generated to predict antioxidative activity of the 25 novel aromatic and heteroaromatic benzamide derivatives. The compounds were tested for antioxidative activity using in vitro spectrophotometric assays. Direct validation of 3D-QSAR approach for predicting activities of novel benzamide derivatives was carried out by comparing experimental and computationally predicted antioxidative activity. Experimentally determined activities for all novel compounds were found to be within a standard deviation of error of the models. Following this, structure-activity relationships among the synthesized compounds are discussed. Furthermore, antiproliferative activity in vitro against HeLa cells as well as antibacterial and antifungal activity was tested to confirm the other biological activities of the prepared compounds.

Preparation and biological evaluation of metronidazole derivatives with monoterpenes and eugenol

Two series of metronidazole derivatives (ester derivatives and ether derivatives) were prepared reacting metronidazole and its acetic acid oxidized form with menthol, thymol, carvacrol, and eugenol. Both series of compounds were tested in vitro against two strains of Helicobacter pylori (the ATCC 26695 and P12), and one strain of Clostridium (Clostridium perfringens). Most of the prepared compounds showed biological activity against the targeted bacteria. Compound 11 was highly active against all tested bacterial strains, especially against P12 with IC₅₀ 0.0011 μM/ml. Compound 6 was highly active against C. perfringens with MIC 0.0094 nM/ml. Viability test was conducted for compound 11 to test its selectivity for normal human fetal lung fibroblasts (MRC5), and it was found to be non-toxic with IC₅₀ more than 50 μM/ml.